I've converted an existing site to multisite with subdomains. There were a few issues to sort out, but it's working well now, with one exception:
Images for the main site are uploading fine, but not for subdomains. For instance, images which should be placed in:
/public_html/wp-content/uploads/sites/6/2016/08
...are ending up in:
/public_html/wp-content/uploads/sites/6/sites/6/2016/08
I suspect the error is in the #uploaded files line below, but I'm not sure what it's doing.
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
# add a trailing slash to /wp-admin
RewriteRule ^wp-admin$ wp-admin/ [R=301,L]
# uploaded files
RewriteRule ^([_0-9a-zA-Z-]+/)?siteN/files/(.+) wp-content/blogs.dir/N/files/$2 [L]
RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule ^(wp-(content|admin|includes).*) $1 [L]
RewriteRule ^(.*\.php)$ $1 [L]
RewriteRule . index.php [L]
# Redirect to www
RewriteCond %{HTTP_HOST} !^www.
RewriteRule ^(.*)$ http://www.%{HTTP_HOST}/$1 [R=301,L]
</IfModule>
# END WordPress
When I move the files to the correct location using FTP, the images appear as they should in the media library.